UNC4: UNC4
In bhklab/MetaGxBreast: Transcriptomic Breast Cancer Datasets
Description
Format
Details
Source
Description
ExpressionSet for the UNC4 Dataset
Format
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experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=20813035
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse18229
PMIDs: 20813035
No abstract available.
notes:
summary:
Clinically, this subtype is usually triple negative invasive ductal carcin
omas with a poor prognosis. Response to standard of care preoperative chem
otherapy is intermediate between basal-like and luminal tumors. The claudi
n-low subtype most closely resembles the mammary epithelial stem cell.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe.10 probe.12 ... probe.79701 (5420 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
Details
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assayData: 5420 features, 305 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
65 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
240.00 51.00 7.73 6.82 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
305 character character
sample_type:
tumor
305
er:
negative positive NA's
99 154 52
pgr:
negative positive NA's
126 109 70
her2:
negative positive NA's
203 58 44
tumor_size:
1 1.5 3 6 NA's
60 1 129 43 72
N:
0 1 NA's
126 135 44
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
24.00 46.00 55.00 56.73 68.00 89.00 59
grade:
1 2 3 NA's
25 80 138 62
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.0 450.0 750.0 954.3 1380.0 3540.0 64
recurrence_status:
norecurrence recurrence NA's
170 70 65
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 540 885 1104 1590 5190 65
vital_status:
deceased living NA's
51 189 65
batch:
UNC4
305
uncurated_author_metadata:
Length Class Mode
305 character character
duplicates:
KOO.KOO_KF_105 KOO.KOO_T01_514 NA's
1 1 303
Source
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse18229
bhklab/MetaGxBreast documentation built on April 29, 2021, 5:20 p.m.
R Package Documentation
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Description Format Details Source
Description
ExpressionSet for the UNC4 Dataset
Format
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=20813035
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse18229
PMIDs: 20813035
No abstract available.
notes:
summary:
Clinically, this subtype is usually triple negative invasive ductal carcin
omas with a poor prognosis. Response to standard of care preoperative chem
otherapy is intermediate between basal-like and luminal tumors. The claudi
n-low subtype most closely resembles the mammary epithelial stem cell.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe.10 probe.12 ... probe.79701 (5420 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
|
Details
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 | assayData: 5420 features, 305 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
65 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
240.00 51.00 7.73 6.82 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
305 character character
sample_type:
tumor
305
er:
negative positive NA's
99 154 52
pgr:
negative positive NA's
126 109 70
her2:
negative positive NA's
203 58 44
tumor_size:
1 1.5 3 6 NA's
60 1 129 43 72
N:
0 1 NA's
126 135 44
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
24.00 46.00 55.00 56.73 68.00 89.00 59
grade:
1 2 3 NA's
25 80 138 62
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.0 450.0 750.0 954.3 1380.0 3540.0 64
recurrence_status:
norecurrence recurrence NA's
170 70 65
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 540 885 1104 1590 5190 65
vital_status:
deceased living NA's
51 189 65
batch:
UNC4
305
uncurated_author_metadata:
Length Class Mode
305 character character
duplicates:
KOO.KOO_KF_105 KOO.KOO_T01_514 NA's
1 1 303
|
Source
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse18229
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